The genetic evolution of populations is an important problem and has been studied extensively over the past few decades. This problem is regaining momentum as more and more detailed genomes of different organisms, which highlight the unexpected diversity within a species, become available. There are two broad directions for studying and understanding this diversity. One direction is through population simulation studies that help hypothesize various evolutionary constraints and conditions, and help understand the observed population structures in that context. The other direction is to reconstruct a plausible evolutionary history given the observed population structure as extant units. In the context of humans, the reconstruction of trees from human genome data under uni-linear transmission, such as non-recombining Y chromosome (NRY) or mitochondrial data, are well accepted. However, evolutionary reconstruction of recombining portions of the genome is a challenge.